MANILA, Philippines (AP) _ The government will file 45 criminal charges against deposed President Ferdinand E. Marcos, but an order barring him from returning from exile may prevent a trial, an official said today.

Ramon Diaz, chairman of the Presidential Commission on Good Government, said the charges against Marcos would be filed later this month, and that Marcos could face life imprisonment if he is convicted on all counts.

But Diaz admitted the government may not be able to proceed with the case because the constitution forbids trials in absentia and President Corazon Aquino has barred Marcos from returning from self-imposed exile in Hawaii.

In other developments in the Philippines today:

-Military leaders said five bombing attacks over the weekend were intended to destabilize Mrs. Aquino's government. Two of the bombing targets were facilities frequented by Americans. No injuries were reported.

-Gen. Fidel Ramos, the armed forces chief of staff, denied Marcos' charge that he illegally acquired $1.25 million from a company run by military veterans. Ramos said that to clear his name, he asked for a probe into sales from a logging concession held by the Veterans Investment Corp. He is the company's chairman of the board.

Marcos was ousted from power Feb. 25, 1986, in a civilian-military revolt that swept Mrs. Aquino to power. Marcos fled the next day to Hawaii.

Diaz said the charges involved 50 Marcos associates along with the former president, his wife, Imelda, and their three children.

The charges include ''pillage, plunder, abuse of authority and abuse of rights'' during Marcos' 20-year rule, Diaz said in an interview. The commission was organized last year to recover Marcos' ''ill-gotten wealth.''

Diaz said the filing of charges will hasten proceedings in Switzerland, where a court last week authorized Swiss officials to help identify funds allegedly stashed in the country by Marcos and his friends.

Marcos was quoted Friday in Honolulu as saying he wants to return home to defend himself against charges by the Aquino government.

''I hereby challenge the Philippine revolutionary government of Madame Aquino to allow me to come home to the Philippines, and allow me to stand trial,'' Marcos told independent film producer Jack Cox, of Abilene, Texas.

Manila Constabulary commander Brig. Gen. Alexander Aguirre said the five bombing attacks over the weekend were ''politically motivated ... their objective is to prevent the convening of Congress.'' Congress opens July 27 for its first session since Marcos abolished the assembly in 1972.

Two grenades exploded Sunday at Notre Dame University in Cotabato City on Mindanao Island, 560 miles south of Manila, where a rebel group, the Moro National Liberation Front, is active. The group has demanded autonomy for Moslems.

On Saturday night, a home-made bomb blasted apart the back of a vintage railroad car inside a historic Spanish fort in Manila.

Shortly before dawn Saturday, unidentified men threw dynamite at a U.S.-run public library and at the largely American International School in the Manila area. Later, a bomb exploded in a concrete garbage bin in Manila's Paco Park.

No one claimed responsibility for any of the attacks.

Aguirre said he put his men on full alert and that he has increased surveillance of suspected extremists.

Ramos held a news conference in Manila to deny charges Marcos made against him in an interview published last week by Asiaweek magazine.

''Let me deny this categorically,'' Ramos said. ''I need not say anything about the credibility of the source (Marcos).''

Ramos is Marcos' cousin. The general, a West Point graduate, was vice chief of staff under Marcos until he helped lead the revolt that toppled Marcos.